Lineage assignment

Pangolin and Nextclade

Lineage assigment table using Pangolin and Nextclade of all samples.

Sample Coverage Pangolin Scorpio Nextclade WHO clade Note
SRR18006914 99.61% B.1.617.2 NA B.1.617.2 Delta Usher placements: B.1.617.2(1/1)
SRR18006924 99.69% B.1.1.529 NA B.1.617.2 Delta Usher placements: B.1.1.529(1/1)
SRR18006919 99.37% B.1.617.2 Delta (B.1.617.2-like) B.1.617.2 Delta Usher placements: B.1.617.2(1/1)
SRR18006917 99.68% B.1.1.529 NA BA.1 Omicron Usher placements: B.1.1.529(1/3) BA.1(1/3) BA.1.15(1/3)
SRR18006920 99.6% AY.39.1.4 Delta (B.1.617.2-like) AY.39.1 Delta Usher placements: AY.39.1.4(1/1)
SRR18006921 90.5% BA.1.17 Omicron (BA.1-like) BA.1.17 Omicron Usher placements: BA.1.17(1/1)
SRR18006916 99.52% B.1.1.529 NA B.1.617.2 Delta Usher placements: B.1.1.529(1/1)
SRR18006913 99.37% B.1.617.2 Delta (B.1.617.2-like) B.1.617.2 Delta Usher placements: AY.39.1.2(1/3) B.1.617.2(2/3)
SRR18006923 99.7% B.1.1.529 NA B.1.617.2 Delta Usher placements: B.1.1.529(1/3) BA.1(1/3) BA.1.15(1/3)

Freyja

The Freyja plot shows the relative SARS-CoV-2 lineage abundance in each sample. Samples suspect for coinfection will illustrate mixed prevalence of two or more variants. The plots below shows the summarized and specific lineages and their corresponding abundance as detected by Freyja.

VirStrain

Samples were analyzed using the VirStrain tool against a database of representative SARS-CoV-2 sequences. The results are summarized in the table below, where the ‘Most Possible Strain’ represents the lineage with the highest Vscore in the initial iteration. Meanwhile, the ‘Other Possible Strain’ is identified by the highest Vscore in subsequent iterations.

Sample Most Possible Strain Other Possible Strain Valid Map Rate
SRR18006914 AY.25_B.1.617.2 Omicron 3/93
SRR18006924 AY.25_B.1.617.2 Omicron 6/93
SRR18006917 Omicron_BA.1 AY.25 6/93
SRR18006923 AY.25_B.1.617.2 Omicron 7/93
SRR18006921 Omicron_BA.1 Can not detect other strains. NA
SRR18006913 AY.25_B.1.617.2 Omicron 4/93
SRR18006919 AY.25_B.1.617.2 Omicron 7/93
SRR18006920 AY.25_B.1.617.2 Can not detect other strains. NA
SRR18006916 AY.43_B.1.617.2 Omicron 7/93

Nucleotide mixture per position

The figure below shows the bammix plot for nucleotide mixtures of the sample/s with potential SARS-CoV-2 variants coinfection. Multiple sites containing heterogenous bases crossing the set threshold (default >20% minor alelle) mixture will be apparent.

Alternative allele fraction

For each lineage-defining mutations

The alternative allele fraction (AAF) determines the number of reads supporting each variant detected in the sample/s. The AAF per mutation of sample/s flagged for SARS-CoV-2 coinfection are shown in the figure.

For each amplicon

The AAF for each amplicon is plotted by getting the average allele fraction for each lineage within the range of that amplicon.

Amplicon sorting

Sample Coverage Pangolin Scorpio Nextclade WHO clade Note
SRR18006916_lineage_A 99.97% AY.39.1.2 Delta (B.1.617.2-like) B.1.617.2 Delta Usher placements: AY.39.1.2(1/1)
SRR18006916_lineage_B 99.95% BA.1.17 Omicron (Unassigned) BA.1.17 Omicron Usher placements: BA.1.17(1/1); scorpio found insufficient support to assign a specific lineage
SRR18006923_lineage_A 99.98% AY.39.1.4 Delta (B.1.617.2-like) AY.39.1 Delta Usher placements: AY.39.1.4(1/1)
SRR18006923_lineage_B 99.98% BA.1.17 Omicron (Unassigned) BA.1.17 Omicron Usher placements: BA.1.17(1/1); scorpio found insufficient support to assign a specific lineage
SRR18006919_lineage_A 99.98% AY.39.1.4 Delta (B.1.617.2-like) B.1.617.2 Delta Usher placements: AY.39.1.4(1/1)
SRR18006919_lineage_B 99.94% BA.1.17 Omicron (Unassigned) BA.1.17 Omicron Usher placements: BA.1.17(1/1); scorpio found insufficient support to assign a specific lineage
SRR18006917_lineage_A 99.98% AY.39.1 Delta (B.1.617.2-like) AY.39.1 Delta Usher placements: AY.39.1(2/2)
SRR18006917_lineage_B 99.98% BA.1.17 Omicron (Unassigned) BA.1.17 Omicron Usher placements: BA.1.17(1/1); scorpio found insufficient support to assign a specific lineage
SRR18006924_lineage_A 99.99% AY.39.1.4 Delta (B.1.617.2-like) AY.39.1 Delta Usher placements: AY.39.1.4(1/1)
SRR18006924_lineage_B 99.97% BA.1.17 Omicron (Unassigned) BA.1.17 Omicron Usher placements: BA.1.17(1/1); scorpio found insufficient support to assign a specific lineage
SRR18006914_lineage_A 99.99% AY.39.1 Delta (B.1.617.2-like) AY.39.1 Delta Usher placements: AY.39.1(2/2)
SRR18006914_lineage_B 99.97% BA.1.17 Omicron (Unassigned) BA.1.17 Omicron Usher placements: BA.1.17(1/2) BA.1.17.2(1/2); scorpio found insufficient support to assign a specific lineage

References

The tools used in this pipeline are as follows: